The effect of 11 common amidinium, imidazolium, and phosphonium based ionic liquids (ILs) on zebrafish (Danio rerio) and Chinese hamster ovary cells (CHO) was investigated with specific emphasis on the effect of anion and cation chain length and aggregation of phosphonium based ILs. Viability and behavioral alteration in the locomotor activity and place preference, after IL treatment of 5 days postfertilization larvae, was recorded. Behavior and histological damage evaluation was performed for adult fish in order to get insight into the long-term effects of two potential biomass-dissolving ILs, [DBNH][OAc] and [P4441][OAc]. To get an understanding of how IL aggregation is linked to the toxicity of ILs, median effective concentrations (EC50) and critical micelle concentrations (CMC) were determined. The long-chain ILs were significantly more toxic than the short-chain ones, and the anion chain length was shown to be less significant than the cation chain length when assessing the impact of ILs on the viability of the organisms. Furthermore, most of the ILs were as monomers when the EC50 was reached. In addition, the ILs used in the long-term tests showed no significant effect on the zebrafish behavior, breeding, or histology, within the used concentration range.